Ice nanotube prisms¶

Figshare: Quasi-1D Nanotube LAMMPS Trajectory (dump-240-square.lammpstrj, 750 TIP4P/2005 waters in a smooth (13,0) tube at 240 K). Tetragonal prism blocks.

The seams CLI has no prism command. Frame.find_prisms writes the engine prism analysis under output_dir.

Python¶

from pydseams import Frame

frame = Frame.from_file("dump-240-square.lammpstrj")
frame.find_prisms(output_dir="output/")

max_depth (default 6) is the largest ring size. shape_matching=True turns on topological unit matching inside the prism search.

Lua¶

require("dseams") does not expose the output-writing prism analysis as a stable helper. The 1.x scripts under example_lua/iceNanotube/ depend on CLI-injected globals. Use Frame.find_prisms for the supported library workflow; low-level Lua registrations are documented in the yodaStruct book.

Howto: confined ice.

References¶

1. The confined-ice topological criterion in the 2020 d-SEAMS paper, doi:10.1021/acs.jcim.0c00031.